Re: [sage-support] gsl in sage outside of notebook
On Wed, Sep 14, 2011 at 2:31 AM, Rajeev Singh rajs2...@gmail.com wrote:
Hi,
The following examples compiles from the notebook
%cython
cimport sage.gsl.ode
import sage.gsl.ode
include 'gsl.pxi'
cdef class van_der_pol(sage.gsl.ode.ode_system):
cdef double beta
def __cinit__(self, double beta=1.0):
self.beta = beta
cdef int c_f(self,double t, double *y,double *dydt):
dydt[0]=y[1]
dydt[1]=-y[0]-self.beta*y[1]*(y[0]*y[0]-1)
return GSL_SUCCESS
cdef int c_j(self, double t,double *y,double *dfdy,double *dfdt):
dfdy[0]=0
dfdy[1]=1.0
dfdy[2]=-2.0*10*y[0]*y[1]-1.0
dfdy[3]=-10*(y[0]*y[0]-1.0)
dfdt[0]=0
dfdt[1]=0
return GSL_SUCCESS
However if I put it in a file vander.pyx (say) and use the following setup.py
-
from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext
ext = Extension(vander, [vander.pyx],
include_dirs = ['/home/rajeev/bin/sage/devel/sage-main/sage/gsl/'])
setup(ext_modules=[ext],
cmdclass = {'build_ext': build_ext})
I get the following error -
cdef class van_der_pol(sage.gsl.ode.ode_system):
^
vander.pyx:10:5: 'ode_system' is not declared
I guess the problem is with the setup.py. Can someone tell me how to do this?
IIRC, the notebook %cython creates a setup.py--you could just look at
that. Chances are your Extension object is missing include dirs and
libraries.
-Robert
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Re: [sage-support] complex parts
On 2011-9-14 23:35, Robert Bradshaw wrote: ... Otherwise, z.real, z.imag is probably going to be as fast as you can get, and there's no need to define a function, you could just write sage: a = complex(3,4) sage: x, y = a.real, a.imag For trivial cases, yeah, but consider parametric_plot((f(t-0.5j).real, f(t-0.5j).imag), (t,tmin,tmax)) parametric_plot(ReIm(f(t-0.5j)), (t,tmin,tmax)) -- Anton Sherwood *\\* www.bendwavy.org *\\* www.zazzle.com/tamfang -- To post to this group, send email to sage-support@googlegroups.com To unsubscribe from this group, send email to sage-support+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-support URL: http://www.sagemath.org
[sage-support] Re: complex parts
For trivial cases, yeah, but consider
parametric_plot((f(t-0.5j).real, f(t-0.5j).imag), (t,tmin,tmax))
parametric_plot(ReIm(f(t-0.5j)), (t,tmin,tmax))
--
For example:
sage: f(z)=[z.real(),z.imag()]
sage: t=var('t')
sage: parametric_plot(f(exp(I*(t-5*I))),(t,0,2*pi))
Andrzej Chrzeszczyk
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[sage-support] Re: Asking whether a number is in QQ or not
b in QQ is (or should be) equivalent to QQ(b) not throwing an error. But if that fails, it only means that Sage can't convert it to a rational directly, it is perfectly possible that after a series of (computationally expensive) steps one could transform b into a rational. But if we would always try every possible simplification then Sage would run very slow. Also, if in were mathematical equivalence, what should Sage return for zeta(5) in QQ? -- To post to this group, send email to sage-support@googlegroups.com To unsubscribe from this group, send email to sage-support+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-support URL: http://www.sagemath.org
[sage-support] Re: for loop in 3d image
A colon is missing after range(20).
The following version works for me:
(but the indentation in this post may be broken)
x,y,z,t = var('x,y,z,t')
P = implicit_plot3d(x^2 +y^2 -z^2 ==1, (x,-3.2,3.2),(y,-3.2,3.2),
(z,-3,3),opacity=.2,color='blue')
for k in range(20):
P += parametric_plot3d([cos((2*pi*k)/(20))+sin((2*pi*k)/
(20))*t,sin((2*pi*k)/(20))-cos((2*pi*k)/(20))*t,t],
(t,-3,3),color='red',thickness=2)
P.show()
Andrzej Chrzeszczyk
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Re: [sage-support] gsl in sage outside of notebook
On Thu, Sep 15, 2011 at 12:07 PM, Robert Bradshaw
rober...@math.washington.edu wrote:
On Wed, Sep 14, 2011 at 2:31 AM, Rajeev Singh rajs2...@gmail.com wrote:
Hi,
The following examples compiles from the notebook
%cython
cimport sage.gsl.ode
import sage.gsl.ode
include 'gsl.pxi'
cdef class van_der_pol(sage.gsl.ode.ode_system):
cdef double beta
def __cinit__(self, double beta=1.0):
self.beta = beta
cdef int c_f(self,double t, double *y,double *dydt):
dydt[0]=y[1]
dydt[1]=-y[0]-self.beta*y[1]*(y[0]*y[0]-1)
return GSL_SUCCESS
cdef int c_j(self, double t,double *y,double *dfdy,double *dfdt):
dfdy[0]=0
dfdy[1]=1.0
dfdy[2]=-2.0*10*y[0]*y[1]-1.0
dfdy[3]=-10*(y[0]*y[0]-1.0)
dfdt[0]=0
dfdt[1]=0
return GSL_SUCCESS
However if I put it in a file vander.pyx (say) and use the following
setup.py -
from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext
ext = Extension(vander, [vander.pyx],
include_dirs = ['/home/rajeev/bin/sage/devel/sage-main/sage/gsl/'])
setup(ext_modules=[ext],
cmdclass = {'build_ext': build_ext})
I get the following error -
cdef class van_der_pol(sage.gsl.ode.ode_system):
^
vander.pyx:10:5: 'ode_system' is not declared
I guess the problem is with the setup.py. Can someone tell me how to do this?
IIRC, the notebook %cython creates a setup.py--you could just look at
that. Chances are your Extension object is missing include dirs and
libraries.
-Robert
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Hi,
The present script takes a pyx file as input and outputs a c, o and so
file in the same directory. The so can now be imported in a sage
program. I have already checked it and its seems to be working fine. I
did look at the commands generated by setup.py file to write this
script.
Rajeev
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[sage-support] Re: Bug in pari/gp or sage? Any fixes?
Hi I have the same problem. I am using sage 4.6 installed on windows vista. This is part of code I have written in sage. Is there anyway I can catch this error and make an exception? Thanks On Sep 13, 9:49 am, vasu tewari.v...@gmail.com wrote: Hi Thanks for the reply. I am also using Sage 4.7.1 installed on Ubuntu 10.04. I installed it using the binary file available at the site. It is weird indeed that you don't end up getting an error! Or am I missing something? On Sep 13, 12:47 am, luisfe lftab...@yahoo.es wrote: On Sep 13, 9:11 am, vasu tewari.v...@gmail.com wrote: Hi all I am trying to run a particular piece of code and it gives an error saying there is a bug in Pari/gp. It turns out that the bug is not present in previous versions of Pari like 2.3.4 (on Windows at least). And if I understand correctly that Sage ships with the newest install of Pari. Is there any way to use the latest Sage version with an old version of Pari?? Any input is appreciated. For those interested, what follows is the code along with the error message. t=gp.thueinit(x^3+21*x^2-2*x-25,1); m=gp.thue(t,1) Hi Vasu, Which version of Sage are you running? Which plattform? How have you installed it? I cannot reproduce your error in Sage 4.7.1 sage: t=gp.thueinit(x^3+21*x^2-2*x-25,1); sage: m=gp.thue(t,1) sage: m [[1, 0]] -- To post to this group, send email to sage-support@googlegroups.com To unsubscribe from this group, send email to sage-support+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-support URL: http://www.sagemath.org
[sage-support] loading a series of files inside a loop
Hi all, I'm new to this group; thanks for having me. I have generated a large number of text files (several lots of 81 files) with the intention of reading them back into another sage program (via the command line). The text filenames were generated by the line outputfilename=Dropbox/simdata_g1%sk%sc%seps%s.sage% (g1int,kint,gridc,grideps) so that the file names have a number of variables, and a typical file is of form simdata_g18k1c2eps3.sage. No problem this far. The files are of a form that should be sage-readable, for instance one line is Lpeak = 0.00101546953017314 I now want to use these files to generate some further output, reading them into a loop as follows: def grid_plot(grid,gamma,kappa): for gridc in [0..8]: for grideps in [0..8]: load 'Dropbox/SAGE-outputs-5genes/gamma5kappa3/ simdata_g15k3c%seps%s.sage'%(cstr,epsstr) blah blah I am hoping to extract and use values such as that of Lpeak above. However while I am able to load a file for particular values of the parameters *outside* the def statement (using exactly the same load statement), I have been unable to make sage run through my files and extract the values inside them. The error I get is: ValueError: argument (='Dropbox/SAGE-outputs-5genes/gamma5kappa3/ simdata_g15k3c%seps%s.sage'%(cstr,epsstr)) to load or attach must have extension py, pyx, sage, spyx, or m Clearly the file does have a correct extension (.sage), as the same command works fine outside the def statement. So is there a problem loading files generically inside a function definition? Is there some other way around this? Thanks, Andrew -- To post to this group, send email to sage-support@googlegroups.com To unsubscribe from this group, send email to sage-support+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-support URL: http://www.sagemath.org
[sage-support] Re: Asking whether a number is in QQ or not
Hi Volker, On 15 Sep., 11:45, Volker Braun vbraun.n...@gmail.com wrote: b in QQ is (or should be) equivalent to QQ(b) not throwing an error. No, that's incorrect. It should be (and is) equivalent to QQ(b)==b returning True. QQ(b) is just a conversion. You can convert any element of a finite prime field into QQ: sage: b = GF(5)(2) sage: QQ(b) 2 However, the test QQ(b)==b is not only testing whether conversion works, but also whether there is a coercion from the ring containing b to QQ. In my example, there is no coercion, thus, no equality: sage: cm.explain(QQ, b.parent()) Will try _r_action and _l_action Unknown result parent. sage: QQ(b) == b False Hence, we have sage: b in QQ False Best regards, Simon -- To post to this group, send email to sage-support@googlegroups.com To unsubscribe from this group, send email to sage-support+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-support URL: http://www.sagemath.org
[sage-support] Re: plot3d with adaptive=True fails
On Sep 15, 9:08 am, Dan Drake dr...@kaist.edu wrote:
This is strange:
x, y =var('x y')
plot3d(sqrt(x^2+y^2)*sin(1/sqrt(x^2+y^2)), (x,-1/2, 1/2), (y, -1/2, 1/2),
adaptive=True)
fails with ValueError: cannot convert float NaN to integer. Something
goes wrong when it partitions up the domain, probably when it looks at
the origin. Is there a way to avoid this? Is this a bug?
Or rather, very very close to the origin. I don't have time right
now, but can you confirm that there is not a depth of recursion
keyword like there is in 2d plotting? I would call this a bug.
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Re: [sage-support] Re: plot3d with adaptive=True fails
On Thu, Sep 15, 2011 at 7:10 PM, kcrisman kcris...@gmail.com wrote:
On Sep 15, 9:08 am, Dan Drake dr...@kaist.edu wrote:
This is strange:
x, y =var('x y')
plot3d(sqrt(x^2+y^2)*sin(1/sqrt(x^2+y^2)), (x,-1/2, 1/2), (y, -1/2, 1/2),
adaptive=True)
fails with ValueError: cannot convert float NaN to integer. Something
goes wrong when it partitions up the domain, probably when it looks at
the origin. Is there a way to avoid this? Is this a bug?
Or rather, very very close to the origin. I don't have time right
now, but can you confirm that there is not a depth of recursion
keyword like there is in 2d plotting? I would call this a bug.
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For the time being there is a hack -
x, y, x1, y1 =var('x y x1 y1')
plot3d(lambda x,y: limit(
limit(sqrt(x1^2+y1^2)*sin(1/sqrt(x1^2+y1^2)), x1=x), y1=y), (x,-1/2,
1/2), (y, -1/2, 1/2), adaptive=True) #slow
or
plot3d(lambda x,y: limit(
limit(sqrt(x1^2+y1^2)*sin(1/sqrt(x1^2+y1^2)), x1=x), y1=y) if
x^2+y^21e-4 else sqrt(x^2+y^2)*sin(1/sqrt(x^2+y^2)), (x,-1/2, 1/2),
(y, -1/2, 1/2), adaptive=True) # dirty but fast
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[sage-support] Re: plot3d with adaptive=True fails
Also:
sage: T = Cylindrical('height', ['radius', 'azimuth'])
sage: r, theta, z = var('r theta z')
sage: plot3d(r*sin(1/r), (r, 0.0, 0.2), (theta, 0, 2*pi),
transformation=T,adaptive=True)
Andrzej Chrzeszczyk
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[sage-support] [ANN} OpenOpt, FuncDesigner, DerApproximator, SpaceFuncs release 0.36
Hi all, new release of our free soft (OpenOpt, FuncDesigner, DerApproximator, SpaceFuncs) v. 0.36 is out: OpenOpt: Now solver interalg can handle all types of constraints and integration problems Some minor improvements and code cleanup FuncDesigner: Interval analysis now can involve min, max and 1-d monotone splines R - R of 1st and 3rd order Some bugfixes and improvements SpaceFuncs: Some minor changes DerApproximator: Some improvements for obtaining derivatives in points from R^n where left or right derivative for a variable is absent, especially for stencil 1 See http://openopt.org for more details. Regards, D. -- To post to this group, send email to sage-support@googlegroups.com To unsubscribe from this group, send email to sage-support+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-support URL: http://www.sagemath.org
[sage-support] Re: Asking whether a number is in QQ or not
PS: sage: cm.explain(QQ, b.parent()) I forgot to copy-and-paste the definition of cm. It was: sage: from sage.structure.element import get_coercion_model sage: cm = get_coercion_model() Cheers, Simon -- To post to this group, send email to sage-support@googlegroups.com To unsubscribe from this group, send email to sage-support+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-support URL: http://www.sagemath.org
Re: [sage-support] Re: plot3d with adaptive=True fails
On Thu, 15 Sep 2011 at 06:40AM -0700, kcrisman wrote:
On Sep 15, 9:08 am, Dan Drake dr...@kaist.edu wrote:
This is strange:
x, y =var('x y')
plot3d(sqrt(x^2+y^2)*sin(1/sqrt(x^2+y^2)), (x,-1/2, 1/2), (y, -1/2, 1/2),
adaptive=True)
fails with ValueError: cannot convert float NaN to integer. Something
goes wrong when it partitions up the domain, probably when it looks at
the origin. Is there a way to avoid this? Is this a bug?
Or rather, very very close to the origin. I don't have time right
now, but can you confirm that there is not a depth of recursion
keyword like there is in 2d plotting? I would call this a bug.
The docstring for plot3d has an (undocumented!) use of initial_depth,
but that didn't solve my problem. I just set plot_points=200 and that
gave me something good enough; switching to cylindrical coordinates also
worked, although I didn't like the look as much.
Dan
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[sage-support] Re: Asking whether a number is in QQ or not
Thank you to all of you! On Sep 15, 12:59 pm, Simon King simon.k...@uni-jena.de wrote: PS: sage: cm.explain(QQ, b.parent()) I forgot to copy-and-paste the definition of cm. It was: sage: from sage.structure.element import get_coercion_model sage: cm = get_coercion_model() Cheers, Simon -- To post to this group, send email to sage-support@googlegroups.com To unsubscribe from this group, send email to sage-support+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-support URL: http://www.sagemath.org
